[English] 日本語
Yorodumi
- PDB-3p0z: Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p0z
TitleCrystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine and FOL955, 4-(1H-imidazol)-1-yl)phenol
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / IspF / cytidine / FOL955 / MEP pathway / isoprene biosynthesis / MSR / metal-binding
Function / homology
Function and homology information


2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / metal ion binding
Similarity search - Function
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, conserved site / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily / YgbB family / 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature. / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / : / 4-(1H-IMIDAZOL-1-YL)PHENOL / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: J Struct Funct Genomics / Year: 2011
Title: Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.
Authors: Begley, D.W. / Hartley, R.C. / Davies, D.R. / Edwards, T.E. / Leonard, J.T. / Abendroth, J. / Burris, C.A. / Bhandari, J. / Myler, P.J. / Staker, B.L. / Stewart, L.J.
#1: Journal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionSep 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
B: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
C: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,62212
Polymers58,4613
Non-polymers1,1619
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-144 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.550, 67.630, 59.770
Angle α, β, γ (deg.)90.00, 95.99, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / MECPS / MECDP-synthase


Mass: 19487.109 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: ispF, BURPS1710b_2511 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3JRA0, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

-
Non-polymers , 6 types, 282 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MSR / 4-(1H-IMIDAZOL-1-YL)PHENOL


Mass: 160.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N2O
#5: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE


Mass: 243.217 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H13N3O5
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 27 mg/mL protein in 20% PEG 4000, 100 mM Tris, 200 mM NaCl, 5 mM ZnCl2. Crystals soaked in 25 mM cytidine and FOLMSR in same buffer for 3 weeks., pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 33803 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.91
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.95-20.4262.1197.5
2-2.060.3322.6199.4
2.06-2.120.2343.9198.8
2.12-2.180.2045.11100
2.18-2.250.2325.9199.5
2.25-2.330.2627.3196.9
2.33-2.420.178.5199.7
2.42-2.520.1859.8198.7
2.52-2.630.13412.2199
2.63-2.760.09714.1199.5
2.76-2.910.09417.3199.5
2.91-3.080.0622.71100
3.08-3.30.0725.5199.2
3.3-3.560.04135.41100
3.56-3.90.0343.9199.7
3.9-4.360.02650.5199.9
4.36-5.030.02257.2199.6
5.03-6.170.02353.6199.8
6.17-8.720.02256.7199.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.83 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.275 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1454 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19102 1712 5.1 %RANDOM
Rwork0.15226 ---
obs0.15425 32038 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.989 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 68 273 3743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213566
X-RAY DIFFRACTIONr_bond_other_d0.0010.022359
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9954848
X-RAY DIFFRACTIONr_angle_other_deg0.94935720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6925465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39723.072153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95415538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4411535
X-RAY DIFFRACTIONr_chiral_restr0.0920.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214069
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02747
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7311.52294
X-RAY DIFFRACTIONr_mcbond_other0.2281.5956
X-RAY DIFFRACTIONr_mcangle_it1.20923622
X-RAY DIFFRACTIONr_scbond_it2.11631272
X-RAY DIFFRACTIONr_scangle_it3.0574.51224
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 118 -
Rwork0.237 2328 -
obs--97.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.01630.47810.43971.79710.63582.236-0.0440.09310.1618-0.18070.0420.0264-0.12460.1080.0020.07540.0095-0.01980.0390.01880.082412.2132-34.8845-13.505
23.28740.28690.01933.4189-0.49440.7614-0.0207-0.24450.59880.2069-0.10340.1398-0.3429-0.07750.12410.19670.012-0.01260.0988-0.06920.20728.2779-25.2723-1.9267
31.6071-0.18860.95850.01450.82373.408-0.06130.14420.03660.0244-0.02050.0798-0.025-0.08130.08180.0931-0.00580.00870.0610.01780.09135.9556-35.8663-17.7926
43.61613.02537.9866-5.62696.289919.89510.04080.82270.53140.1291-0.2679-0.1514-0.6236-1.53280.2270.44420.1686-0.05890.62870.09780.5236-3.3162-24.8798-16.905
51.84150.23020.42920.8513-0.29151.39920.0421-0.0206-0.02620.00110.03360.03090.0823-0.0993-0.07580.06940.00080.01950.02070.01180.03285.7105-39.6873-9.8431
61.9391-0.2802-1.28023.6227-0.78291.73240.0467-0.1965-0.11640.23410.0484-0.09920.14540.1092-0.09510.10050.01220.00160.07410.01060.06467.5112-40.679-0.0906
72.55482.0297-0.13153.5653-0.40991.25680.0296-0.16610.01650.1612-0.085-0.0938-0.010.13860.05530.09730.0082-0.00840.0417-0.0030.064518.4054-36.1794-4.5712
82.62912.69481.44997.01432.72372.371-0.07690.07640.0193-0.07390.06280.0010.03780.07310.0140.07440.00680.00470.02620.01690.04413.2873-39.3087-13.3653
93.45922.01153.91055.3312.700511.05370.43010.8499-0.64470.4669-0.0750.09730.7557-0.0973-0.35510.20270.0717-0.02160.1655-0.17570.285620.4691-57.4014-19.0988
102.20570.36561.17483.3232-0.15992.0239-0.26360.72420.4297-0.19680.1454-0.1305-0.31420.49680.11820.0945-0.10480.03220.35380.14840.146224.2532-28.8782-30.3723
119.696110.74049.240914.8024-7.83769.0561-0.35860.97820.60670.1301-0.1014-0.1157-0.19830.84580.460.1841-0.16430.03780.57940.26880.230326.7947-24.7277-32.2281
123.069-0.18620.87621.6904-1.13830.2643-0.02980.6934-0.0297-0.35920.0291-0.2470.22940.34130.00070.13550.04740.05720.3842-0.06420.104327.4807-43.1126-26.6354
1318.169-2.83161.56712.22890.34983.4349-0.42271.22280.7682-0.06430.2016-0.5297-0.6231-0.18760.22110.3170.01870.11990.5557-0.06320.30831.3735-42.7288-33.2807
145.8051.9276-0.12780.4009-2.05566.09710.06671.0121-0.4264-0.1716-0.2271-0.41350.17180.85510.16030.23030.11260.08120.5261-0.17890.206926.2202-51.2548-32.5255
151.90860.30391.20871.50850.48351.5534-0.07820.4250.1884-0.0958-0.00150.073-0.09860.33170.07970.0608-0.02270.01560.14850.04770.044616.1216-34.6539-26.0242
160.50541.27751.60247.0679-2.88634.33230.27890.5816-0.3671-0.08330.0013-0.09280.7230.4018-0.28020.18310.1565-0.07110.1738-0.14970.149619.2289-55.982-24.0201
175.03782.8530.1654.2507-0.20590.74910.07420.117-0.08540.15810.0147-0.13830.08710.1774-0.08890.11270.0462-0.00250.0575-0.01540.060925.4468-42.2599-7.9763
182.9012-0.5025-0.0989.71692.24833.37620.0268-0.19390.24540.4173-0.1053-0.8312-0.1540.43490.07840.09090.0158-0.07610.17910.01260.236642.048-37.6794-5.9122
191.8063-0.54921.11550.7183-0.23540.8170.0506-0.0576-0.16320.20620.046-0.12590.06280.009-0.09660.15460.0453-0.02580.08150.01050.120125.2225-45.7813-4.0234
2029.01510.3819-7.18672.1375-0.34576.0908-0.1884-2.77720.75110.64920.2918-0.3385-0.06770.422-0.10340.37890.078-0.10720.3349-0.07540.208629.3278-45.55495.3747
211.3618-0.16270.31911.2294-0.80441.72130.05560.0196-0.28240.07930.0179-0.1130.19010.1792-0.07350.10890.0726-0.02560.0592-0.00440.114628.0015-50.7849-5.6131
222.3668-0.01750.7054.9838-1.02332.01970.16370.453-0.174-0.2771-0.2507-0.37940.2570.46310.08710.10120.11430.02760.18950.00850.161138.8319-47.757-13.4508
232.5250.05410.56452.99880.02971.4531-0.08160.40180.0169-0.04330.0702-0.23950.06650.45820.01140.0510.02460.00680.16050.00820.058531.7412-39.8044-15.1383
2426.702513.4244-8.614715.6621-2.76968.44230.5149-0.5954-1.35351.1269-0.4358-0.41960.6058-0.1663-0.07910.30790.0206-0.04750.04630.04310.218316.7273-58.4664-7.9119
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 18
2X-RAY DIFFRACTION2A19 - 38
3X-RAY DIFFRACTION3A39 - 64
4X-RAY DIFFRACTION4A65 - 72
5X-RAY DIFFRACTION5A73 - 108
6X-RAY DIFFRACTION6A109 - 122
7X-RAY DIFFRACTION7A123 - 145
8X-RAY DIFFRACTION8A146 - 158
9X-RAY DIFFRACTION9B1 - 5
10X-RAY DIFFRACTION10B6 - 29
11X-RAY DIFFRACTION11B30 - 38
12X-RAY DIFFRACTION12B39 - 60
13X-RAY DIFFRACTION13B61 - 76
14X-RAY DIFFRACTION14B77 - 93
15X-RAY DIFFRACTION15B94 - 153
16X-RAY DIFFRACTION16B154 - 159
17X-RAY DIFFRACTION17C1 - 17
18X-RAY DIFFRACTION18C18 - 39
19X-RAY DIFFRACTION19C40 - 58
20X-RAY DIFFRACTION20C59 - 74
21X-RAY DIFFRACTION21C75 - 103
22X-RAY DIFFRACTION22C104 - 122
23X-RAY DIFFRACTION23C123 - 154
24X-RAY DIFFRACTION24C155 - 159

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more